The changes in the layout has been made by the Builder for the convenience of the investors as per the municipal records the building design only recognises 1 and 2 BHK flats based on the previous layouts and electrical connection has been issued in the same manner to identify the property as two units so the society will also charts for two units.

Has change in building plans been approved by muncipal corporation 

2) if building plans show 2 flats and 2 share certificate issued fir separate flat society can charge you separate maintenance for each flat 

1. Well, maintenance fees are determined s per the area of the flat and not on the number of flats occupied by the share holder.

2. So in your case the amount of maintenance would be anyway more due to are two flats in combination covers.

3. The logic of the society is not baseless due to original design of the flat sand 2 share certificates issued by the society.

So I do not think you can manage to convince the society about the single entity of the 2 flats merged together.

Why have 2 share certificate been issued by society ?

what is mentioned in building sanctioned plans ? 

If builder has got plans changed and sold one flat then you ought to be charged maintenance  for only one flat 

1) Need to check layout passed by PMC and Completion certificate.

2) If its one unit in OC than you need to pay maintenance for 1 flat only.

You need to check the sanctioned building plans to check whether builder amended the plan to convert the two flats into a single unit

If that is so, then society cannot charge separate maintenance for two flats

1. As per the information mentioned in the present query, makes it clear that though the two flats have been merged into one, but there is only one sale deed for that whole area.
2. Let me tell you that it is irrespective of the fact that previously these were two separate flats, but now being made as one and only one sale deed is also there, it should only be considered as one unit.
3. The society is not corret in charging the double maitenance charges considering this flat as two different units.

This is illegal. The nature of the said flat has to be mentioned in DA or PAAA stating it's exact position. As per your description this will be termed as single flat only 

If you are using the larger area than other member you will have to pay more maintainence as per the norm. 

It can be seen as one unit only.

Three meters are not title documents neither there's any reason for issuing two share certificates for a single unit.

You may request the association to merge both the certificates into one and get it issued.

The builder's help may be sought if association do not cooperate.

If the association is not accepting your request then you may have to file a declaratory suit to declare it as a single unit and to direct the association to merge the two certificates into one 

You may even issue a legal notice in this regard to test their pulse.

01. Please check the Approval plan. If you are charged property tax for 2 flats, then you are liable to pay two maintenance.

02. As you have separate EB meter means surely as per approved plan, it will be separate property tax. So you are liable to pay maintenance for both flats, even tough you have one entrance. 

03. one Sale agreement for any number properties can registered. Your sale deed cant be taken as single unit as it has two door numbers itself in one sale agreement.

Dear Sir,

You will be considered as owner and in possession of single unit as per single sale deed which is existing.  Lodge a complaint with Deputy registrar for not following the rules and also approach civil court if necessary.